@itkoren/sqmd 0.1.0

package/dist/ingestion/parser.js

@@ -0,0 +1,98 @@
+import * as path from 'node:path';
+import remarkParse from 'remark-parse';
+import { unified } from 'unified';
+function extractNodeText(node) {
+    const parts = [];
+    if ('value' in node && typeof node.value === 'string') {
+        parts.push(node.value);
+    }
+    if ('children' in node && Array.isArray(node.children)) {
+        for (const child of node.children) {
+            parts.push(extractNodeText(child));
+        }
+    }
+    return parts.join('');
+}
+function getNodeStart(node) {
+    return node.position?.start?.line ?? 0;
+}
+function getNodeEnd(node) {
+    return node.position?.end?.line ?? 0;
+}
+export function parseMarkdown(content, filePath) {
+    const processor = unified().use(remarkParse);
+    const ast = processor.parse(content);
+    const sections = [];
+    const headingStack = [];
+    let currentSectionNodes = [];
+    let currentSectionStart = 1;
+    let currentHeadingLevel = 0;
+    let currentHeadingText = '';
+    function flushSection(endLine) {
+        const sectionText = currentSectionNodes
+            .map((n) => extractNodeText(n))
+            .filter((t) => t.trim().length > 0)
+            .join('\n\n');
+        const parentHeadings = headingStack.map((h) => h.text);
+        const headingPath = headingStack.length > 0 ? headingStack.map((h) => h.text).join(' > ') : '';
+        sections.push({
+            headingPath,
+            headingText: currentHeadingText,
+            headingLevel: currentHeadingLevel,
+            lineStart: currentSectionStart,
+            lineEnd: endLine,
+            content: sectionText,
+            parentHeadings: [...parentHeadings],
+        });
+        currentSectionNodes = [];
+    }
+    const children = ast.children;
+    let i = 0;
+    while (i < children.length) {
+        const node = children[i];
+        if (node.type === 'heading') {
+            const headingNode = node;
+            const level = headingNode.depth;
+            const headingText = extractNodeText(headingNode);
+            const lineStart = getNodeStart(headingNode);
+            // Flush previous section
+            if (currentSectionNodes.length > 0 || currentHeadingLevel > 0) {
+                flushSection(lineStart - 1);
+            }
+            // Update heading stack
+            // Pop headings at same or deeper level
+            while (headingStack.length > 0 && headingStack[headingStack.length - 1].level >= level) {
+                headingStack.pop();
+            }
+            // Push current heading to parent stack for next sections
+            currentHeadingLevel = level;
+            currentHeadingText = headingText;
+            currentSectionStart = lineStart;
+            // The heading itself becomes the first node
+            currentSectionNodes = [headingNode];
+            // Push to stack for children headings
+            headingStack.push({ level, text: headingText });
+        }
+        else {
+            if (currentSectionNodes.length === 0 && sections.length === 0 && headingStack.length === 0) {
+                // Preamble content before first heading
+                currentSectionStart = getNodeStart(node);
+            }
+            currentSectionNodes.push(node);
+        }
+        i++;
+    }
+    // Flush last section
+    if (currentSectionNodes.length > 0 || (sections.length === 0 && children.length > 0)) {
+        const lastLine = children.length > 0 ? getNodeEnd(children[children.length - 1]) : 0;
+        flushSection(lastLine);
+    }
+    return {
+        filePath,
+        sections,
+    };
+}
+export function getFileStem(filePath) {
+    return path.basename(filePath, path.extname(filePath));
+}
+//# sourceMappingURL=parser.js.map

package/dist/ingestion/parser.js.map

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package/dist/ingestion/pipeline.d.ts

@@ -0,0 +1,32 @@
+import type { Config } from '../config/schema.js';
+export interface FileError {
+    filePath: string;
+    error: string;
+}
+export interface IndexResult {
+    indexed: number;
+    skipped: number;
+    errors: FileError[];
+}
+export type ProgressCallback = (event: {
+    type: 'file_start' | 'file_done' | 'file_skip' | 'file_error' | 'batch_embed';
+    filePath?: string;
+    indexed?: number;
+    skipped?: number;
+    errors?: number;
+    total?: number;
+}) => void;
+export interface RunOptions {
+    paths: string[];
+    force?: boolean;
+    onProgress?: ProgressCallback;
+    concurrency?: number;
+}
+export declare class IndexPipeline {
+    private config;
+    private embedder;
+    constructor(config: Config);
+    private getEmbedder;
+    run(options: RunOptions): Promise<IndexResult>;
+}
+//# sourceMappingURL=pipeline.d.ts.map

package/dist/ingestion/pipeline.d.ts.map

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package/dist/ingestion/pipeline.js

@@ -0,0 +1,191 @@
+import * as fs from 'node:fs';
+import pLimit from 'p-limit';
+import { OllamaEmbedder } from '../embeddings/ollama.js';
+import { TransformersEmbedder } from '../embeddings/transformers.js';
+import { createIndexes, getChunksTable, getDb, getFilesTable } from '../store/db.js';
+import { getAllFiles } from '../store/reader.js';
+import { upsertChunks, upsertFile } from '../store/writer.js';
+import { chunkDocument } from './chunker.js';
+import { hashFile, hashPath } from './fingerprint.js';
+import { parseMarkdown } from './parser.js';
+import { scanDirectory } from './scanner.js';
+export class IndexPipeline {
+    config;
+    embedder = null;
+    constructor(config) {
+        this.config = config;
+    }
+    getEmbedder() {
+        if (this.embedder)
+            return this.embedder;
+        const { backend, model, ollama_base_url } = this.config.embeddings;
+        if (backend === 'ollama') {
+            this.embedder = new OllamaEmbedder(model, ollama_base_url);
+        }
+        else {
+            this.embedder = new TransformersEmbedder(model, this.config.paths.model_cache_dir);
+        }
+        return this.embedder;
+    }
+    async run(options) {
+        const { paths, force = false, onProgress, concurrency = 4 } = options;
+        const db = await getDb(this.config.paths.db_path);
+        const chunksTable = await getChunksTable(db);
+        const filesTable = await getFilesTable(db);
+        // Build map of existing file hashes
+        const existingFiles = await getAllFiles(filesTable);
+        const existingHashMap = new Map(existingFiles.map((f) => [f.file_id, f.file_hash]));
+        const { extensions, ignore_patterns } = this.config.watcher;
+        // Collect all files to process
+        const filesToProcess = [];
+        for (const searchPath of paths) {
+            if (!fs.existsSync(searchPath)) {
+                console.warn(`Path not found: ${searchPath}`);
+                continue;
+            }
+            const stat = fs.statSync(searchPath);
+            if (stat.isDirectory()) {
+                for await (const filePath of scanDirectory(searchPath, extensions, ignore_patterns)) {
+                    filesToProcess.push(filePath);
+                }
+            }
+            else if (stat.isFile()) {
+                const ext = searchPath.match(/\.[^.]+$/)?.[0]?.toLowerCase() ?? '';
+                if (extensions.includes(ext)) {
+                    filesToProcess.push(searchPath);
+                }
+            }
+        }
+        const result = {
+            indexed: 0,
+            skipped: 0,
+            errors: [],
+        };
+        const limit = pLimit(concurrency);
+        const embedder = this.getEmbedder();
+        const { batch_size } = this.config.embeddings;
+        let pendingChunks = [];
+        let pendingFiles = [];
+        const flushBatch = async () => {
+            if (pendingChunks.length === 0)
+                return;
+            // Embed all pending chunks
+            const texts = pendingChunks.map((c) => c.text);
+            const batchCount = Math.ceil(texts.length / batch_size);
+            for (let b = 0; b < batchCount; b++) {
+                const start = b * batch_size;
+                const end = Math.min(start + batch_size, texts.length);
+                const batchTexts = texts.slice(start, end);
+                const embeddings = await embedder.embed(batchTexts);
+                for (let i = 0; i < batchTexts.length; i++) {
+                    pendingChunks[start + i].vector = embeddings[i];
+                }
+                onProgress?.({ type: 'batch_embed', total: end });
+            }
+            // Upsert chunks
+            for (let i = 0; i < pendingFiles.length; i++) {
+                const file = pendingFiles[i];
+                const fileChunks = pendingChunks.filter((c) => c.file_id === file.file_id);
+                await upsertChunks(chunksTable, fileChunks);
+                await upsertFile(filesTable, file);
+                result.indexed++;
+                onProgress?.({
+                    type: 'file_done',
+                    filePath: file.file_path,
+                    indexed: result.indexed,
+                    skipped: result.skipped,
+                    errors: result.errors.length,
+                });
+            }
+            pendingChunks = [];
+            pendingFiles = [];
+        };
+        const processFile = async (filePath) => {
+            onProgress?.({ type: 'file_start', filePath });
+            const fileId = hashPath(filePath);
+            const { hash: fileHash, mtime: fileMtime } = await hashFile(filePath);
+            // Skip unchanged files unless force
+            if (!force && existingHashMap.get(fileId) === fileHash) {
+                result.skipped++;
+                onProgress?.({
+                    type: 'file_skip',
+                    filePath,
+                    skipped: result.skipped,
+                });
+                return;
+            }
+            const content = fs.readFileSync(filePath, 'utf-8');
+            const doc = parseMarkdown(content, filePath);
+            const chunks = chunkDocument(doc, {
+                fileId,
+                fileHash,
+                filePath,
+                fileMtime,
+                maxTokens: this.config.chunking.max_tokens,
+                minChars: this.config.chunking.min_chars,
+                overlapTokens: this.config.chunking.overlap_tokens,
+                includeBreadcrumb: this.config.chunking.include_breadcrumb,
+            });
+            const fileRecord = {
+                file_id: fileId,
+                file_path: filePath,
+                file_hash: fileHash,
+                file_mtime: fileMtime,
+                chunk_count: chunks.length,
+                indexed_at: Date.now(),
+                status: 'indexed',
+                error_msg: '',
+            };
+            pendingChunks.push(...chunks);
+            pendingFiles.push(fileRecord);
+        };
+        // Process files with concurrency limit
+        const tasks = filesToProcess.map((filePath) => limit(async () => {
+            try {
+                await processFile(filePath);
+            }
+            catch (err) {
+                result.errors.push({
+                    filePath,
+                    error: err instanceof Error ? err.message : String(err),
+                });
+                onProgress?.({
+                    type: 'file_error',
+                    filePath,
+                    errors: result.errors.length,
+                });
+                // Record error in files table
+                const fileId = hashPath(filePath);
+                const fileRecord = {
+                    file_id: fileId,
+                    file_path: filePath,
+                    file_hash: '',
+                    file_mtime: 0,
+                    chunk_count: 0,
+                    indexed_at: Date.now(),
+                    status: 'error',
+                    error_msg: err instanceof Error ? err.message : String(err),
+                };
+                try {
+                    await upsertFile(filesTable, fileRecord);
+                }
+                catch {
+                    // Best effort
+                }
+            }
+            // Flush when we have enough chunks
+            if (pendingChunks.length >= batch_size * 4) {
+                await flushBatch();
+            }
+        }));
+        await Promise.all(tasks);
+        // Final flush
+        await flushBatch();
+        // Create indexes after bulk loading
+        if (result.indexed > 0) {
+            await createIndexes(db);
+        }
+        return result;
+    }
+}
+//# sourceMappingURL=pipeline.js.map

package/dist/ingestion/pipeline.js.map

@@ -0,0 +1 @@
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package/dist/ingestion/scanner.d.ts

@@ -0,0 +1,2 @@
+export declare function scanDirectory(dir: string, extensions: string[], ignorePatterns?: string[]): AsyncGenerator<string>;
+//# sourceMappingURL=scanner.d.ts.map

package/dist/ingestion/scanner.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"scanner.d.ts","sourceRoot":"","sources":["../../src/ingestion/scanner.ts"],"names":[],"mappings":"AAqBA,wBAAuB,aAAa,CAClC,GAAG,EAAE,MAAM,EACX,UAAU,EAAE,MAAM,EAAE,EACpB,cAAc,GAAE,MAAM,EAAyC,GAC9D,cAAc,CAAC,MAAM,CAAC,CAaxB"}

package/dist/ingestion/scanner.js

@@ -0,0 +1,54 @@
+import * as fs from 'node:fs';
+import * as path from 'node:path';
+function matchesPattern(filePath, pattern) {
+    // Convert glob pattern to regex
+    const escaped = pattern
+        .replace(/[.+^${}()|[\]\\]/g, '\\$&')
+        .replace(/\*\*/g, '<<DOUBLE_STAR>>')
+        .replace(/\*/g, '[^/]*')
+        .replace(/\?/g, '[^/]')
+        .replace(/<<DOUBLE_STAR>>/g, '.*');
+    const regex = new RegExp(escaped);
+    return regex.test(filePath) || regex.test(filePath.replace(/\\/g, '/'));
+}
+function matchesAnyPattern(filePath, patterns) {
+    const normalizedPath = filePath.replace(/\\/g, '/');
+    return patterns.some((pattern) => matchesPattern(normalizedPath, pattern));
+}
+export async function* scanDirectory(dir, extensions, ignorePatterns = ['**/.git/**', '**/node_modules/**']) {
+    const normalizedDir = path.resolve(dir);
+    if (!fs.existsSync(normalizedDir)) {
+        return;
+    }
+    const stat = fs.statSync(normalizedDir);
+    if (!stat.isDirectory()) {
+        return;
+    }
+    yield* walkDirectory(normalizedDir, extensions, ignorePatterns);
+}
+async function* walkDirectory(dir, extensions, ignorePatterns) {
+    let entries;
+    try {
+        entries = fs.readdirSync(dir, { withFileTypes: true });
+    }
+    catch {
+        return;
+    }
+    for (const entry of entries) {
+        const fullPath = path.join(dir, entry.name);
+        const normalizedPath = fullPath.replace(/\\/g, '/');
+        if (matchesAnyPattern(normalizedPath, ignorePatterns)) {
+            continue;
+        }
+        if (entry.isDirectory()) {
+            yield* walkDirectory(fullPath, extensions, ignorePatterns);
+        }
+        else if (entry.isFile()) {
+            const ext = path.extname(entry.name).toLowerCase();
+            if (extensions.includes(ext)) {
+                yield fullPath;
+            }
+        }
+    }
+}
+//# sourceMappingURL=scanner.js.map

package/dist/ingestion/scanner.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"scanner.js","sourceRoot":"","sources":["../../src/ingestion/scanner.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,SAAS,CAAC;AAC9B,OAAO,KAAK,IAAI,MAAM,WAAW,CAAC;AAElC,SAAS,cAAc,CAAC,QAAgB,EAAE,OAAe;IACvD,gCAAgC;IAChC,MAAM,OAAO,GAAG,OAAO;SACpB,OAAO,CAAC,mBAAmB,EAAE,MAAM,CAAC;SACpC,OAAO,CAAC,OAAO,EAAE,iBAAiB,CAAC;SACnC,OAAO,CAAC,KAAK,EAAE,OAAO,CAAC;SACvB,OAAO,CAAC,KAAK,EAAE,MAAM,CAAC;SACtB,OAAO,CAAC,kBAAkB,EAAE,IAAI,CAAC,CAAC;IAErC,MAAM,KAAK,GAAG,IAAI,MAAM,CAAC,OAAO,CAAC,CAAC;IAClC,OAAO,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,CAAC;AAC1E,CAAC;AAED,SAAS,iBAAiB,CAAC,QAAgB,EAAE,QAAkB;IAC7D,MAAM,cAAc,GAAG,QAAQ,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;IACpD,OAAO,QAAQ,CAAC,IAAI,CAAC,CAAC,OAAO,EAAE,EAAE,CAAC,cAAc,CAAC,cAAc,EAAE,OAAO,CAAC,CAAC,CAAC;AAC7E,CAAC;AAED,MAAM,CAAC,KAAK,SAAS,CAAC,CAAC,aAAa,CAClC,GAAW,EACX,UAAoB,EACpB,iBAA2B,CAAC,YAAY,EAAE,oBAAoB,CAAC;IAE/D,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;IAExC,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,aAAa,CAAC,EAAE,CAAC;QAClC,OAAO;IACT,CAAC;IAED,MAAM,IAAI,GAAG,EAAE,CAAC,QAAQ,CAAC,aAAa,CAAC,CAAC;IACxC,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE,EAAE,CAAC;QACxB,OAAO;IACT,CAAC;IAED,KAAK,CAAC,CAAC,aAAa,CAAC,aAAa,EAAE,UAAU,EAAE,cAAc,CAAC,CAAC;AAClE,CAAC;AAED,KAAK,SAAS,CAAC,CAAC,aAAa,CAC3B,GAAW,EACX,UAAoB,EACpB,cAAwB;IAExB,IAAI,OAAoB,CAAC;IAEzB,IAAI,CAAC;QACH,OAAO,GAAG,EAAE,CAAC,WAAW,CAAC,GAAG,EAAE,EAAE,aAAa,EAAE,IAAI,EAAE,CAAC,CAAC;IACzD,CAAC;IAAC,MAAM,CAAC;QACP,OAAO;IACT,CAAC;IAED,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE,CAAC;QAC5B,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC;QAC5C,MAAM,cAAc,GAAG,QAAQ,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;QAEpD,IAAI,iBAAiB,CAAC,cAAc,EAAE,cAAc,CAAC,EAAE,CAAC;YACtD,SAAS;QACX,CAAC;QAED,IAAI,KAAK,CAAC,WAAW,EAAE,EAAE,CAAC;YACxB,KAAK,CAAC,CAAC,aAAa,CAAC,QAAQ,EAAE,UAAU,EAAE,cAAc,CAAC,CAAC;QAC7D,CAAC;aAAM,IAAI,KAAK,CAAC,MAAM,EAAE,EAAE,CAAC;YAC1B,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,WAAW,EAAE,CAAC;YACnD,IAAI,UAAU,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC7B,MAAM,QAAQ,CAAC;YACjB,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC"}

package/dist/mcp/server.d.ts

@@ -0,0 +1,8 @@
+import type * as lancedb from '@lancedb/lancedb';
+import type { Config } from '../config/schema.js';
+import type { Embedder } from '../embeddings/types.js';
+export declare function startMcpServer(db: lancedb.Connection, embedder: Embedder, config: Config, options?: {
+    transport?: 'stdio' | 'sse';
+    port?: number;
+}): Promise<void>;
+//# sourceMappingURL=server.d.ts.map

package/dist/mcp/server.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"server.d.ts","sourceRoot":"","sources":["../../src/mcp/server.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,KAAK,OAAO,MAAM,kBAAkB,CAAC;AAIjD,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,qBAAqB,CAAC;AAClD,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,wBAAwB,CAAC;AAGvD,wBAAsB,cAAc,CAClC,EAAE,EAAE,OAAO,CAAC,UAAU,EACtB,QAAQ,EAAE,QAAQ,EAClB,MAAM,EAAE,MAAM,EACd,OAAO,GAAE;IAAE,SAAS,CAAC,EAAE,OAAO,GAAG,KAAK,CAAC;IAAC,IAAI,CAAC,EAAE,MAAM,CAAA;CAAO,GAC3D,OAAO,CAAC,IAAI,CAAC,CAiFf"}

package/dist/mcp/server.js

@@ -0,0 +1,73 @@
+import { createServer } from 'node:http';
+import { Server } from '@modelcontextprotocol/sdk/server/index.js';
+import { SSEServerTransport } from '@modelcontextprotocol/sdk/server/sse.js';
+import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
+import { registerTools } from './tools.js';
+export async function startMcpServer(db, embedder, config, options = {}) {
+    const transport = options.transport ?? config.mcp.transport;
+    const port = options.port ?? config.mcp.sse_port;
+    const server = new Server({
+        name: 'sqmd',
+        version: '0.1.0',
+    }, {
+        capabilities: {
+            tools: {},
+            resources: {},
+        },
+    });
+    // Register all tools and resources
+    registerTools(server, db, embedder, config);
+    if (transport === 'stdio') {
+        console.error('[mcp] Starting stdio transport');
+        const stdioTransport = new StdioServerTransport();
+        await server.connect(stdioTransport);
+        console.error('[mcp] Server connected via stdio');
+    }
+    else if (transport === 'sse') {
+        console.log(`[mcp] Starting SSE transport on port ${port}`);
+        const httpServer = createServer();
+        const sseTransports = new Map();
+        httpServer.on('request', (req, res) => {
+            const url = new URL(req.url ?? '/', `http://localhost:${port}`);
+            if (req.method === 'GET' && url.pathname === '/sse') {
+                const sseTransport = new SSEServerTransport('/messages', res);
+                const sessionId = Date.now().toString();
+                sseTransports.set(sessionId, sseTransport);
+                res.on('close', () => {
+                    sseTransports.delete(sessionId);
+                });
+                server.connect(sseTransport).catch((err) => {
+                    console.error('[mcp] SSE connection error:', err instanceof Error ? err.message : String(err));
+                });
+            }
+            else if (req.method === 'POST' && url.pathname === '/messages') {
+                // Find the matching SSE transport
+                for (const sseTransport of sseTransports.values()) {
+                    sseTransport.handlePostMessage(req, res).catch((err) => {
+                        console.error('[mcp] Message handling error:', err instanceof Error ? err.message : String(err));
+                    });
+                    return;
+                }
+                res.writeHead(404);
+                res.end('No active SSE connection');
+            }
+            else {
+                res.writeHead(404);
+                res.end('Not found');
+            }
+        });
+        await new Promise((resolve, reject) => {
+            httpServer.listen(port, () => {
+                console.log(`[mcp] SSE server listening on http://localhost:${port}/sse`);
+                resolve();
+            });
+            httpServer.on('error', reject);
+        });
+        // Keep alive
+        await new Promise(() => { });
+    }
+    else {
+        throw new Error(`Unknown transport: ${transport}`);
+    }
+}
+//# sourceMappingURL=server.js.map

package/dist/mcp/server.js.map

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package/dist/mcp/tools.d.ts

@@ -0,0 +1,6 @@
+import type * as lancedb from '@lancedb/lancedb';
+import type { Server } from '@modelcontextprotocol/sdk/server/index.js';
+import type { Config } from '../config/schema.js';
+import type { Embedder } from '../embeddings/types.js';
+export declare function registerTools(server: Server, db: lancedb.Connection, embedder: Embedder, config: Config): void;
+//# sourceMappingURL=tools.d.ts.map

package/dist/mcp/tools.d.ts.map

@@ -0,0 +1 @@
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